[gmx-users] Partial incompatibility of pdb2gmx with 4 character residue names?
joerg.sauter at mpikg.mpg.de
Thu Aug 15 15:45:56 CEST 2013
I am building a tetramer of beta(1-4) linked glucose with pdb2gmx
(Gromacs 4.6.3). I have three residue types BGLB BGLM BGLE defined in
the aminoacids.rtp with which I want to built the chain BGLB BGLM BGLM BGLE.
Using pdb2gmx works fine, until I link the residues via the specbond.dat
BGLB O4 1 BGLM C1 1 0.147 BGLB BGLM
BGLM O4 1 BGLM C1 1 0.147 BGLM BGLM
BGLM O4 1 BGLE C1 1 0.147 BGLM BGLE
In this case I get the error message:
Atom HO4 in residue BGLE 4 was not found in rtp entry BGLM with 21 atoms
while sorting atoms.
Using the -debug 1 mode I found that internally (in the chain.pdb) the
residue names get shortened to BGL thus making the residues
indistinguishable. Therefore, pdb2gmx seems to mix up residues resulting
in the error above. If I use residue names consisting of only 3
characters everything works fine again.
Is this behaviour known or intended? I could not find any note on this
in the manual and it took me some time to figure this out, so maybe
there should be at least a warning.
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